null Sun 23 Dec 22:23:10 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr8-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-1.8-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-1.8-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:20 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-1.8-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 174 and 0 Target number of residues in the AU: 174 Target solvent content: 0.4443 Checking the provided sequence file Detected sequence length: 142 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 142 Adjusted target solvent content: 0.55 Input MTZ file: 1vr8-1.8-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 154 Cell parameters: 57.762 57.762 87.976 90.000 90.000 120.000 Input sequence file: 1vr8-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1136 target number of atoms Had to go as low as 0.35 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 50.023 1.751 Wilson plot Bfac: 13.49 16611 reflections ( 94.45 % complete ) and 0 restraints for refining 1267 atoms. Observations/parameters ratio is 3.28 ------------------------------------------------------ Starting model: R = 0.3094 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2612 (Rfree = 0.000) for 1267 atoms. Found 63 (63 requested) and removed 31 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.67 1.56 Round 1: 127 peptides, 5 chains. Longest chain 47 peptides. Score 0.890 Round 2: 129 peptides, 3 chains. Longest chain 74 peptides. Score 0.919 Round 3: 130 peptides, 3 chains. Longest chain 57 peptides. Score 0.921 Round 4: 130 peptides, 4 chains. Longest chain 57 peptides. Score 0.909 Round 5: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Taking the results from Round 5 Chains 2, Residues 129, Estimated correctness of the model 99.7 % 2 chains (129 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1331 restraints for refining 1320 atoms. 169 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2697 (Rfree = 0.000) for 1320 atoms. Found 57 (66 requested) and removed 36 (33 requested) atoms. Cycle 2: After refmac, R = 0.2429 (Rfree = 0.000) for 1337 atoms. Found 46 (66 requested) and removed 24 (33 requested) atoms. Cycle 3: After refmac, R = 0.2131 (Rfree = 0.000) for 1357 atoms. Found 46 (65 requested) and removed 15 (34 requested) atoms. Cycle 4: After refmac, R = 0.1995 (Rfree = 0.000) for 1382 atoms. Found 41 (66 requested) and removed 25 (34 requested) atoms. Cycle 5: After refmac, R = 0.1934 (Rfree = 0.000) for 1392 atoms. Found 51 (65 requested) and removed 23 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.64 1.53 Round 1: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 2: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 3: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 4: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 5: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Taking the results from Round 5 Chains 2, Residues 129, Estimated correctness of the model 99.7 % 2 chains (129 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1341 restraints for refining 1369 atoms. 179 conditional restraints added. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2019 (Rfree = 0.000) for 1369 atoms. Found 64 (64 requested) and removed 35 (34 requested) atoms. Cycle 7: After refmac, R = 0.1956 (Rfree = 0.000) for 1395 atoms. Found 30 (63 requested) and removed 26 (34 requested) atoms. Cycle 8: After refmac, R = 0.1849 (Rfree = 0.000) for 1399 atoms. Found 54 (63 requested) and removed 23 (35 requested) atoms. Cycle 9: After refmac, R = 0.1834 (Rfree = 0.000) for 1429 atoms. Found 32 (64 requested) and removed 34 (35 requested) atoms. Cycle 10: After refmac, R = 0.1817 (Rfree = 0.000) for 1421 atoms. Found 46 (62 requested) and removed 28 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.65 1.54 Round 1: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 2: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 3: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 4: 133 peptides, 3 chains. Longest chain 77 peptides. Score 0.925 Round 5: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Taking the results from Round 5 Chains 2, Residues 132, Estimated correctness of the model 99.7 % 2 chains (132 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1358 restraints for refining 1383 atoms. 196 conditional restraints added. Observations/parameters ratio is 3.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1919 (Rfree = 0.000) for 1383 atoms. Found 59 (59 requested) and removed 36 (34 requested) atoms. Cycle 12: After refmac, R = 0.1865 (Rfree = 0.000) for 1403 atoms. Found 37 (59 requested) and removed 21 (35 requested) atoms. Cycle 13: After refmac, R = 0.1808 (Rfree = 0.000) for 1418 atoms. Found 37 (58 requested) and removed 23 (35 requested) atoms. Cycle 14: After refmac, R = 0.1762 (Rfree = 0.000) for 1432 atoms. Found 39 (57 requested) and removed 23 (35 requested) atoms. Cycle 15: After refmac, R = 0.1741 (Rfree = 0.000) for 1444 atoms. Found 46 (56 requested) and removed 25 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.65 1.54 Round 1: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 2: 130 peptides, 3 chains. Longest chain 74 peptides. Score 0.921 Round 3: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 4: 130 peptides, 3 chains. Longest chain 74 peptides. Score 0.921 Round 5: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Taking the results from Round 5 Chains 2, Residues 129, Estimated correctness of the model 99.7 % 2 chains (129 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1373 restraints for refining 1385 atoms. 211 conditional restraints added. Observations/parameters ratio is 3.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1904 (Rfree = 0.000) for 1385 atoms. Found 52 (52 requested) and removed 35 (34 requested) atoms. Cycle 17: After refmac, R = 0.1846 (Rfree = 0.000) for 1401 atoms. Found 52 (52 requested) and removed 23 (35 requested) atoms. Cycle 18: After refmac, R = 0.1794 (Rfree = 0.000) for 1428 atoms. Found 53 (53 requested) and removed 30 (35 requested) atoms. Cycle 19: After refmac, R = 0.1767 (Rfree = 0.000) for 1449 atoms. Found 42 (52 requested) and removed 30 (36 requested) atoms. Cycle 20: After refmac, R = 0.1727 (Rfree = 0.000) for 1457 atoms. Found 49 (51 requested) and removed 29 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.65 1.54 Round 1: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 2: 133 peptides, 3 chains. Longest chain 77 peptides. Score 0.925 Round 3: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 4: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 5: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Taking the results from Round 5 Chains 2, Residues 132, Estimated correctness of the model 99.7 % 2 chains (132 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1360 restraints for refining 1384 atoms. 198 conditional restraints added. Observations/parameters ratio is 3.00 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1930 (Rfree = 0.000) for 1384 atoms. Found 47 (47 requested) and removed 35 (34 requested) atoms. Cycle 22: After refmac, R = 0.1806 (Rfree = 0.000) for 1394 atoms. Found 46 (46 requested) and removed 18 (34 requested) atoms. Cycle 23: After refmac, R = 0.1755 (Rfree = 0.000) for 1419 atoms. Found 45 (47 requested) and removed 24 (35 requested) atoms. Cycle 24: After refmac, R = 0.1770 (Rfree = 0.000) for 1437 atoms. Found 37 (46 requested) and removed 25 (36 requested) atoms. Cycle 25: After refmac, R = 0.1745 (Rfree = 0.000) for 1443 atoms. Found 45 (45 requested) and removed 33 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.65 1.54 Round 1: 131 peptides, 3 chains. Longest chain 75 peptides. Score 0.922 Round 2: 132 peptides, 2 chains. Longest chain 75 peptides. Score 0.935 Round 3: 132 peptides, 2 chains. Longest chain 75 peptides. Score 0.935 Round 4: 132 peptides, 2 chains. Longest chain 75 peptides. Score 0.935 Round 5: 131 peptides, 3 chains. Longest chain 75 peptides. Score 0.922 Taking the results from Round 4 Chains 2, Residues 130, Estimated correctness of the model 99.7 % 2 chains (130 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1386 restraints for refining 1400 atoms. 224 conditional restraints added. Observations/parameters ratio is 2.97 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1913 (Rfree = 0.000) for 1400 atoms. Found 42 (42 requested) and removed 37 (35 requested) atoms. Cycle 27: After refmac, R = 0.1814 (Rfree = 0.000) for 1402 atoms. Found 41 (41 requested) and removed 15 (35 requested) atoms. Cycle 28: After refmac, R = 0.1777 (Rfree = 0.000) for 1426 atoms. Found 39 (41 requested) and removed 25 (35 requested) atoms. Cycle 29: After refmac, R = 0.1760 (Rfree = 0.000) for 1438 atoms. Found 40 (40 requested) and removed 22 (36 requested) atoms. Cycle 30: After refmac, R = 0.1737 (Rfree = 0.000) for 1453 atoms. Found 39 (39 requested) and removed 26 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.64 1.53 Round 1: 131 peptides, 3 chains. Longest chain 75 peptides. Score 0.922 Round 2: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 3: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 4: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Round 5: 134 peptides, 2 chains. Longest chain 77 peptides. Score 0.937 Taking the results from Round 5 Chains 2, Residues 132, Estimated correctness of the model 99.7 % 2 chains (132 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1351 restraints for refining 1388 atoms. 189 conditional restraints added. Observations/parameters ratio is 2.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1927 (Rfree = 0.000) for 1388 atoms. Found 36 (36 requested) and removed 35 (34 requested) atoms. Cycle 32: After refmac, R = 0.1817 (Rfree = 0.000) for 1388 atoms. Found 34 (34 requested) and removed 12 (34 requested) atoms. Cycle 33: After refmac, R = 0.1772 (Rfree = 0.000) for 1406 atoms. Found 35 (35 requested) and removed 12 (35 requested) atoms. Cycle 34: After refmac, R = 0.1739 (Rfree = 0.000) for 1429 atoms. Found 35 (35 requested) and removed 17 (35 requested) atoms. Cycle 35: After refmac, R = 0.1733 (Rfree = 0.000) for 1447 atoms. Found 36 (36 requested) and removed 28 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.66 1.55 Round 1: 130 peptides, 3 chains. Longest chain 74 peptides. Score 0.921 Round 2: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 3: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 4: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 5: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Taking the results from Round 5 Chains 2, Residues 129, Estimated correctness of the model 99.7 % 2 chains (129 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 86 A 1 chains (136 residues) following loop building 1 chains (136 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1365 restraints for refining 1392 atoms. 203 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1900 (Rfree = 0.000) for 1392 atoms. Found 34 (34 requested) and removed 33 (34 requested) atoms. Cycle 37: After refmac, R = 0.1808 (Rfree = 0.000) for 1391 atoms. Found 34 (34 requested) and removed 20 (34 requested) atoms. Cycle 38: After refmac, R = 0.1743 (Rfree = 0.000) for 1403 atoms. Found 35 (35 requested) and removed 17 (35 requested) atoms. Cycle 39: After refmac, R = 0.1711 (Rfree = 0.000) for 1421 atoms. Found 35 (35 requested) and removed 27 (35 requested) atoms. Cycle 40: After refmac, R = 0.1695 (Rfree = 0.000) for 1427 atoms. Found 35 (35 requested) and removed 19 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.65 1.54 Round 1: 131 peptides, 3 chains. Longest chain 74 peptides. Score 0.922 Round 2: 132 peptides, 2 chains. Longest chain 74 peptides. Score 0.935 Round 3: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 4: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 5: 131 peptides, 3 chains. Longest chain 74 peptides. Score 0.922 Taking the results from Round 2 Chains 3, Residues 130, Estimated correctness of the model 99.7 % 2 chains (127 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 86 A 2 chains (137 residues) following loop building 1 chains (134 residues) in sequence following loop building ------------------------------------------------------ 16611 reflections ( 94.45 % complete ) and 1378 restraints for refining 1389 atoms. 222 conditional restraints added. Observations/parameters ratio is 2.99 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1931 (Rfree = 0.000) for 1389 atoms. Found 34 (34 requested) and removed 38 (34 requested) atoms. Cycle 42: After refmac, R = 0.1808 (Rfree = 0.000) for 1385 atoms. Found 34 (34 requested) and removed 15 (34 requested) atoms. Cycle 43: After refmac, R = 0.1769 (Rfree = 0.000) for 1403 atoms. Found 35 (35 requested) and removed 22 (35 requested) atoms. Cycle 44: After refmac, R = 0.1716 (Rfree = 0.000) for 1414 atoms. Found 35 (35 requested) and removed 27 (35 requested) atoms. Cycle 45: After refmac, R = 0.1710 (Rfree = 0.000) for 1420 atoms. Found 35 (35 requested) and removed 21 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.66 1.55 Round 1: 131 peptides, 2 chains. Longest chain 74 peptides. Score 0.933 Round 2: 132 peptides, 2 chains. Longest chain 75 peptides. Score 0.935 Round 3: 132 peptides, 2 chains. Longest chain 75 peptides. Score 0.935 Round 4: 131 peptides, 3 chains. Longest chain 64 peptides. Score 0.922 Round 5: 132 peptides, 2 chains. Longest chain 75 peptides. Score 0.935 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 130, Estimated correctness of the model 99.7 % 2 chains (130 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 78 A and 86 A 1 chains (137 residues) following loop building 1 chains (137 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 16611 reflections ( 94.45 % complete ) and 1171 restraints for refining 1138 atoms. Observations/parameters ratio is 3.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2566 (Rfree = 0.000) for 1138 atoms. Found 28 (28 requested) and removed 0 (28 requested) atoms. Cycle 47: After refmac, R = 0.2316 (Rfree = 0.000) for 1138 atoms. Found 29 (29 requested) and removed 0 (29 requested) atoms. Cycle 48: After refmac, R = 0.2138 (Rfree = 0.000) for 1138 atoms. Found 25 (29 requested) and removed 0 (29 requested) atoms. Cycle 49: After refmac, R = 0.2012 (Rfree = 0.000) for 1138 atoms. Found 10 (30 requested) and removed 1 (30 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:14 GMT 2018 Job finished. TimeTaking 33.07 Used memory is bytes: 14419104